I also tested the 3d editing toolbar in ArcScene and all I had in the scene was 2d polygons and I had no problem editing them. To convert features into 3d, I'm assuming you were trying this with the 3d analyst toolbar, and not the 3d editing toolbar. Almost all the functions have been removed from the toolbar, so you need access to the Geoprocessing tool equivalent. To turn on ArcToolbox inside ArcScene, go to Customize > Customize Mode > Commands tab and type ArcToolbox. Drag the toolbox icon onto any existing toolbar and then proceed to the 3D Analyst toolbox. Optionally, you can go to Geoprocessing (main menu) > Search for Tools. If you have indexed your system tools, Search will find the tool you are looking for. In this case, to convert features to 3d, you want to use the Interpolate Shape tool.
Hope this helps!
Eric Rice
Development Technical Lead
User Advocacy Group
ESRI Support Services